I had to download each airport separately and then install the download manager each time to get them to work
If with "download manager", you mean the Stand-Alone Addon Manager installer, it's totally unnecessary, since the current scenery installers will do everything needed. The only case where you must run the Stand-Alone Addon Manager, is if you, AFTER having migrated a scenery, install another one using an OLD installer so, in that case, you should either download the new scenery installer, or the Stand-Alone Addon Manager, and only once, after installing a product using an old installer.
My question; since they are in a different drive can I point P3D4 at them in the scenery library or do I have to download each into P3D 4? Hope that makes sense.
I'm not sure I understand the question. If you had P3D V4 installed when you run the scenery installers AND you had Prepar3D v4 checked in the installer options, the sceneries will surely work in it, without doing anything, regardless of the drive you installed into.